Preheat oven to 425 degrees F. Line baking sheet with foil.
Toss butternut squash with 2 tablespoon oil, cinnamon, and season with salt.
Place onto prepared baking sheet and bake in preheated oven for 40 minutes, or until squash is tender.
Meanwhile, in large sauce pan, cook chopped bacon until completely cooked.
Remove from pan and set aside.
Remove drippings from pan and add remaining 1 tablespoon olive oil.
Over medium heat, add onions and cook until soft, about 10 minutes, stirring often.
Cook pasta according to package.
Reserve 1 cup of pasta water.
Once butternut squash is done, place in blender along with half of the onions, nutmeg, and milk.
Puree until well blended.
Pour pureed squash into saucepan with remaining onions over low heat and add cheese.
Stir until cheese is melted.
Add cooked pasta to sauce and toss to combine. Add reserved pasta water, 1 tablespoon at a time if sauce is too thick, to reach desired consistency of sauce.
Season with salt and pepper according to taste.
Top with bacon crumbles and enjoy!